Detecting Relationships between Amino Acid Residue Sequences and 3D Protein Structures based on a New Class of Rotamer Libraries

In the past a good number of rotamer libraries have been published, which allow a deeper understanding of the conformational behaviour of amino acid residues in proteins. Since the number of available high resolution X-ray protein structures has grown significantly over the last years, a more comprehensive analysis of the conformational behaviour is possible today. In this paper, we present a method to compile a new class of rotamer libraries for detecting interesting relationships between residue conformations and their sequential context in proteins. The method is based on a new algorithm for clustering residue conformations. To demonstrate the effectivity of our method we apply our algorithm to a library consisting of all 8000 tripetid fragments formed by the 20 native amino acids. The analysis shows some very interesting new results, namely that some specific tripeptid fragments show some unexpected conformation of residues instead of the highly preferred conformation. In the neighborhood of two asparagin residues, for example, threonin avoids the conformation which is most likely to occur otherwise. The new insights obtained by the analysis are important in understanding the formation and prevention of secondary structure elements and will consequently be crucial for improving the state-of-the-art of protein folding

Detecting Relationships between Amino Acid Residue Sequences and 3D Protein Structures based on a New Class of Rotamer Libraries

In the past a good number of rotamer libraries have been published, which allow a deeper understanding of the conformational behaviour of amino acid residues in proteins. Since the number of available high resolution X-ray protein structures has grown significantly over the last years, a more comprehensive analysis of the conformational behaviour is possible today. In this paper, we present a method to compile a new class of rotamer libraries for detecting interesting relationships between residue conformations and their sequential context in proteins. The method is based on a new algorithm for clustering residue conformations. To demonstrate the effectivity of our method we apply our algorithm to a library consisting of all 8000 tripetid fragments formed by the 20 native amino acids. The analysis shows some very interesting new results, namely that some specific tripeptid fragments show some unexpected conformation of residues instead of the highly preferred conformation. In the neigh..